My daughter has some trouble reading music, so I try sometimes to help with the soprano recorder. The instrument is quite old, Johannes Adler written on it. Alone it sounds quite nice but with the violin (tuned) it sounds terrible! Completely out of tune. Do I do something wrong or is it the recorder? My daughter plays in pitch (I know she often plays along with the CD)
The recorder is probably very poor - Adlers were made in what was East Germany and in my opinion were not well-designed or well made. In fact, you may have a German-fingered recorder which are all uniformly terrible. The fingering for low f-natural is usually T1234-67, i.e, forked, but for those German fingered recorders it's T12345. In order to make this fingering work the tuning for the rest of the notes is severely compromised. But if even this is an English/Baroque/Modern fingered recorder, it is very likely out of tune with itself. If you've never had it worked on then getting it to play in tune may not be possible.
If you don't take our advice and get a tenor, at least go buy a new Yamaha plastic soprano. The clear colored ones work well, although you can see your spit in them.
Note also the soprano sounds in a very high range. Your lowest note is C5, only a third lower than the E string. It is very difficult even for professionals to match pitches up there perfectly and because the pitches are so high being even a little off can be very upsetting. That's one reason why piccolo players are often grouped in threes, it's easier for 3 of them to get in tune than just 2.
Sounds like the violin is in tune, but the recorder is out of tune. It's most likely just the recorder. There may be a couple of possibilities here. Try to determine how far out of tune (and in which direction) the recorder is, either using a tuner or by ear.
Recorders can be tuned by pulling out the head joint from the body. If the recorder's pitch is too high, this will lower it. If the recorder's pitch is already too low, I'm not there's much you can do (unless the head joint is already pulled out, in which case you can push it back in).
Recorders (especially sopranos) are also susceptible to changing pitch along with breath pressure, so the harder you blow, the sharper the pitch gets, and the softer you blow, the lower it gets (this is why recorders don't have much dynamic range -- it makes them play out of tune). It's possible that you're blowing to hard or soft, and that by blowing harder or softer, you can bend the pitch into an acceptable range. But this is generally a pretty minor effect, and it sounds like your problem is much larger.
It's also possible that the recorder may be pitched in A=415 pitch, which is the tuning standard used by historical Baroque performance. Modern pitch (which her violin would be tuned to) is A=440. This results in a half-step difference. So if she plays an open E string (in a=440), you would have to play an F (in a=415) to get the same sound. This would be inconvenient. See also: How can I play my new tenor recorder (a'=440) along with someone playing a harpsichord (a'=415)?
Well, assuming that you tuned the violin properly to the flute (it may work better to tune to something other than A though), the basic advice here is: don't play empty strings.
A recorder has a very straight and pure tone and sort of a compromise tuning. It takes very experienced recorder players to even slightly adjust pitch.
It takes "only" a good violin player to adjust pitch automatically, and once you add vibrato (and thus lose the straight and pure tone from the violin), the beatings get masked anyway.
But in a nutshell my experience is: when playing with recorder players below the semiprofessional level, don't bother playing an empty string on your violin ever. You cannot tune the violin well enough to have that work out.
Note there are two different 20th-century designs of recorder, "German" and "baroque". You can tell the difference by looking at the relative size of the finger holes - see http://www.mollenhauer.com/en/useful-information/recorder-designs/baroque-and-german-fingering#.VcU2nZDbKJA.
You can't play in tune using the "wrong" fingering for the instrument. The German design was invented to be simpler for absolute beginners (you play the basic diatonic scale of the instrument simply by uncovering the holes one by one) but it is not so good for chromatic notes. And since they were designed as very cheap beginner's instruments, "German" recorders are often not good quality instruments in any case.
Fingering charts for the two basic types (and a lot more besides) are here: http://www.recorder-fingerings.com/en/index.php